Selecting Stable Molecular Targets for Treatment and Prevention of AIDS

Yaoyu E Wang[1] (yew@bu.edu)
Chao Zhang[2] (czhang@plexxikon.com)
Jay Berzofsky[3] (berzofsk@HELIX.NIH.GOV)
Charles DeLisi[1],[2] (delisi@bu.edu)

[1]Departments of Bioinformatics , Boston University, Boston Massachusetts, 02215
[2]Biomedical Engineering , Boston University, Boston Massachusetts, 02215
[3]Vaccine Branch, Center for Cancer Research, National Cancer Institute, NIH

Abstract

The common consideration in approaching protection against HIV, whether by a vaccine or therapeutic, is identification of suitable targets. Among the central criteria for suitability is target stability; i.e. resistance to mutation. In this paper we address the problem of stability, and develop methods for identifying stable targets. The targets that we focus on are structures formed by viral peptides and products of the class I major histocompatibility complex, the target of the immune system. The method mines the large databases of fully sequenced HIV genomes and MHC binding peptides, and takes account of human polymorphism to construct hundreds of subpopulation specific stable targets, each consisting of combinations of 3-5 complexes.

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